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Package 372/514HostnameOS / ArchBUILDCHECKBUILD BIN
PICS 1.8.0
Arnaud Droit
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/PICS
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: PICS
Version: 1.8.0
Command: rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_1.8.0.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R PICS.buildbin-libdir
StartedAt: 2012-03-24 05:31:10 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 05:31:49 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:  OK 
PackageFile: PICS_1.8.0.tgz
PackageFileSize: 1.64 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_1.8.0.tar.gz'
>>>>>>> 

* installing *source* package 'PICS' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'background':
background.c:44: warning: statement with no effect
background.c:97: warning: statement with no effect
background.c:12: warning: unused variable 'length'
background.c:10: warning: unused variable 'countR'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:804: warning: suggest parentheses around comparison in operand of &
pics.c:964: warning: suggest parentheses around comparison in operand of &
pics.c:652: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010: warning: unused variable 'ee'
pics.c:1010: warning: unused variable 'ggR'
pics.c:1010: warning: unused variable 'ggF'
pics.c:1010: warning: unused variable 'aaR'
pics.c:1010: warning: unused variable 'aaF'
pics.c:1010: warning: unused variable 'etaDiff'
pics.c:1001: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634: warning: unused variable 'PhiRw'
pics.c:1634: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890: warning: unused variable 'j'
pics.c:1890: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421: warning: 'firstFit' may be used uninitialized in this function
pics.c:421: warning: 'ans' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106: warning: suggest parentheses around comparison in operand of &
segment.c:97: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:248: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461: warning: suggest parentheses around comparison in operand of &
segment.c:1462: warning: suggest parentheses around comparison in operand of &
segment.c:1463: warning: suggest parentheses around comparison in operand of &
segment.c:1464: warning: suggest parentheses around comparison in operand of &
segment.c:1465: warning: suggest parentheses around comparison in operand of &
segment.c:1466: warning: suggest parentheses around comparison in operand of &
segment.c:1467: warning: suggest parentheses around comparison in operand of &
segment.c:1409: warning: unused variable 'filter1'
segment.c:1408: warning: unused variable 'muFilter'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PICS.so background.o pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386
** R
** inst
** preparing package for lazy loading
in method for 'as.list' with signature '"AlignedRead"': no definition for class "AlignedRead"
in method for 'coerce' with signature '"AlignedRead","GenomeData"': no definition for class "AlignedRead"
Creating a generic function for 'density' from package 'stats' in package 'PICS'
Creating a generic function for 'plot' from package 'graphics' in package 'PICS'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'PICS.Rnw' 
** testing if installed package can be loaded

* DONE (PICS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR PICS.buildbin-libdir/PICS/libs/i386/PICS.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=PICS.buildbin-libdir --libs-only PICS_1.8.0.tar.gz'
>>>>>>> 

* installing *source* package 'PICS' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'background':
background.c:44: warning: statement with no effect
background.c:97: warning: statement with no effect
background.c:12: warning: unused variable 'length'
background.c:10: warning: unused variable 'countR'
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:804: warning: suggest parentheses around comparison in operand of &
pics.c:964: warning: suggest parentheses around comparison in operand of &
pics.c:652: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010: warning: unused variable 'ee'
pics.c:1010: warning: unused variable 'ggR'
pics.c:1010: warning: unused variable 'ggF'
pics.c:1010: warning: unused variable 'aaR'
pics.c:1010: warning: unused variable 'aaF'
pics.c:1010: warning: unused variable 'etaDiff'
pics.c:1001: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634: warning: unused variable 'PhiRw'
pics.c:1634: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890: warning: unused variable 'j'
pics.c:1890: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421: warning: 'firstFit' may be used uninitialized in this function
pics.c:421: warning: 'ans' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106: warning: suggest parentheses around comparison in operand of &
segment.c:97: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:248: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461: warning: suggest parentheses around comparison in operand of &
segment.c:1462: warning: suggest parentheses around comparison in operand of &
segment.c:1463: warning: suggest parentheses around comparison in operand of &
segment.c:1464: warning: suggest parentheses around comparison in operand of &
segment.c:1465: warning: suggest parentheses around comparison in operand of &
segment.c:1466: warning: suggest parentheses around comparison in operand of &
segment.c:1467: warning: suggest parentheses around comparison in operand of &
segment.c:1409: warning: unused variable 'filter1'
segment.c:1408: warning: unused variable 'muFilter'
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PICS.so background.o pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/ppc

* DONE (PICS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR PICS.buildbin-libdir/PICS/libs/ppc/PICS.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=PICS.buildbin-libdir --libs-only PICS_1.8.0.tar.gz'
>>>>>>> 

* installing *source* package 'PICS' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'background':
background.c:44: warning: statement with no effect
background.c:97: warning: statement with no effect
background.c:12: warning: unused variable 'length'
background.c:10: warning: unused variable 'countR'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:804: warning: suggest parentheses around comparison in operand of &
pics.c:964: warning: suggest parentheses around comparison in operand of &
pics.c:652: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010: warning: unused variable 'ee'
pics.c:1010: warning: unused variable 'ggR'
pics.c:1010: warning: unused variable 'ggF'
pics.c:1010: warning: unused variable 'aaR'
pics.c:1010: warning: unused variable 'aaF'
pics.c:1010: warning: unused variable 'etaDiff'
pics.c:1001: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634: warning: unused variable 'PhiRw'
pics.c:1634: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890: warning: unused variable 'j'
pics.c:1890: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421: warning: 'firstFit' may be used uninitialized in this function
pics.c:421: warning: 'ans' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106: warning: suggest parentheses around comparison in operand of &
segment.c:97: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:248: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461: warning: suggest parentheses around comparison in operand of &
segment.c:1462: warning: suggest parentheses around comparison in operand of &
segment.c:1463: warning: suggest parentheses around comparison in operand of &
segment.c:1464: warning: suggest parentheses around comparison in operand of &
segment.c:1465: warning: suggest parentheses around comparison in operand of &
segment.c:1466: warning: suggest parentheses around comparison in operand of &
segment.c:1467: warning: suggest parentheses around comparison in operand of &
segment.c:1409: warning: unused variable 'filter1'
segment.c:1408: warning: unused variable 'muFilter'
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PICS.so background.o pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/x86_64

* DONE (PICS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"